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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 20:25:11 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.63     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_step0-01A_R00_1-64A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-63A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-63A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0941
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6300
  Estimated number of reflections :      34473
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.6300

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_step0-01A_R00_1-64A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.039 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.199 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.833 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.227 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.429 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.396 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.137 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:22-OCT-19
  --------------------------------
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections       1354
Number of   all  reflections      26560
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          26560

   Current auto weighting coefficient =    6.5747271    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.899 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   76
 Minimum acceptable grid spacing:    81   81  172
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   76
 Minimum acceptable grid spacing:    81   81  172
 Weight matrix   0.30095705    
 Actual weight    6.5747271      is applied to the X-ray term
Norm of X_ray positional gradient                37.3
Norm of Geom. positional gradient                82.8
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.147E+08
 Cosine of angle between them                      -0.491
Product of X_ray and Geom B-fact gradients     -0.358E+08
 Cosine of angle between them                      -0.877


Residuals: XRAY=     0.8423E+06 GEOM=     0.1367E+05 TOTAL=     0.8560E+06
 function value    856013.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.861     1.644
Bond angles  : others                          3238     2.371     1.580
Torsion angles, period  1. refined              185     6.813     5.000
Torsion angles, period  2. refined               90    34.978    22.778
Torsion angles, period  3. refined              268    13.151    15.000
Torsion angles, period  4. refined                9    12.558    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   301     0.246     0.200
VDW repulsions.others                          1343     0.219     0.200
VDW; torsion: refined_atoms                     727     0.174     0.200
VDW; torsion.others                             723     0.082     0.200
HBOND: refined_atoms                            208     0.208     0.200
HBOND.others                                      2     0.042     0.200
VDW repulsions: symmetry: refined_atoms           8     0.209     0.200
VDW repulsions: symmetry: others                 23     0.203     0.200
HBOND: symmetry: refined_atoms                   21     0.170     0.200
M. chain bond B values: refined atoms           746     1.741     1.460
M. chain bond B values: others                  746     1.737     1.461
M. chain angle B values: refined atoms          929     2.706     2.181
M. chain angle B values: others                 930     2.705     2.181
S. chain bond B values: refined atoms           811     3.113     1.861
S. chain bond B values: others                  810     3.108     1.860
S. chain angle B values: refined atoms         1177     4.739     2.624
S. chain angle B values: others                1178     4.737     2.623
Long range B values: refined atoms             1839     7.153    20.216
Long range B values: others                    1750     6.855    18.820
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =    0.0925
Partial structure    1: scale =     0.3869, B  =   42.1493
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.048    3427 100.00   439.1   448.3  0.16  0.17     158   439.7   448.9  0.20  0.21
 0.141    5763  99.98   269.1   255.3  0.17  0.15     333   274.4   254.0  0.23  0.20
 0.235    7390  99.99   179.0   161.8  0.18  0.16     400   182.8   166.4  0.21  0.18
 0.329    8616 100.00    79.8    93.8  0.30  0.23     463    74.8    89.4  0.35  0.28
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0475   2485   0.912    942   0.811   3427   0.884  0.950  0.9623  0.9696  0.9045  0.9373
  0.1415   4829   0.865    934   0.760   5763   0.848  1.010  0.9414  0.9553  0.8823  0.9385
  0.2355   6440   0.874    950   0.765   7390   0.860  1.057  0.9528  0.9587  0.9091  0.9407
  0.3294   7683   0.731    941   0.649   8624   0.722  0.761  0.8725  0.8985  0.8243  0.8842
 $$
Resolution limits                    =     41.964     1.630
Number of used reflections           =      25202
Percentage observed                  =    99.9887
Percentage of free reflections       =     5.0987
Overall R factor                     =     0.1881
Free R factor                        =     0.2304
Average Fourier shell correlation    =     0.9388
AverageFree Fourier shell correlation=     0.9236
Overall weighted R factor            =     0.1657
Free weighted R factor               =     0.2047
Overall weighted R2 factor           =     0.1970
Free weighted R2 factor              =     0.2412
Average correlation coefficient      =     0.9204
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9343
Cruickshanks DPI for coordinate error=     0.1001
DPI based on free R factor           =     0.1032
Overall figure of merit              =     0.8133
ML based su of positional parameters =     0.0716
ML based su of thermal parameters    =     2.1519
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    128117.98       13673.082       856013.81      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37616476    
 Actual weight    6.5747271      is applied to the X-ray term


 function value    844713.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =   -0.0600
Partial structure    1: scale =     0.3869, B  =   42.1787
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1883
Free R factor                        =     0.2299
Average Fourier shell correlation    =     0.9472
AverageFree Fourier shell correlation=     0.9337
Average correlation coefficient      =     0.9194
Overall figure of merit              =     0.8437
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    127168.90       8612.2656       844713.06       856013.81    


     CGMAT cycle number =      3

 Weight matrix   0.38350525    
 Actual weight    6.5747271      is applied to the X-ray term


 function value    844281.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =   -0.0066
Partial structure    1: scale =     0.3870, B  =   42.1737
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1878
Free R factor                        =     0.2301
Average Fourier shell correlation    =     0.9481
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9203
Overall figure of merit              =     0.8467
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    127049.59       8965.3955       844281.75       844713.06    


     CGMAT cycle number =      4

 Weight matrix   0.38362929    
 Actual weight    6.5747271      is applied to the X-ray term


 function value    844232.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =   -0.0020
Partial structure    1: scale =     0.3869, B  =   42.1420
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1879
Free R factor                        =     0.2302
Average Fourier shell correlation    =     0.9482
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9206
Overall figure of merit              =     0.8470
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    127027.34       9062.0576       844232.13       844281.75    


     CGMAT cycle number =      5

 Weight matrix   0.38342571    
 Actual weight    6.5747271      is applied to the X-ray term


 function value    844232.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =   -0.0002
Partial structure    1: scale =     0.3866, B  =   41.8562
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1879
Free R factor                        =     0.2301
Average Fourier shell correlation    =     0.9482
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9207
Overall figure of merit              =     0.8470
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    127022.34       9096.1875       844234.94       844232.13    

 fvalues    127022.34       9096.1875       844232.06       844233.38    
 fvalues    127022.34       9096.1875       844232.06       844233.38    


     CGMAT cycle number =      6

 Weight matrix   0.38326818    
 Actual weight    6.5747271      is applied to the X-ray term


 function value    844228.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =    0.0003
Partial structure    1: scale =     0.3865, B  =   41.7917
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1879
Free R factor                        =     0.2301
Average Fourier shell correlation    =     0.9482
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9207
Overall figure of merit              =     0.8470
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    127020.97       9100.0791       844228.25       844233.38    


     CGMAT cycle number =      7

 Weight matrix   0.38308924    
 Actual weight    6.5747271      is applied to the X-ray term


 function value    844237.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =    0.0001
Partial structure    1: scale =     0.3865, B  =   41.7939
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1879
Free R factor                        =     0.2302
Average Fourier shell correlation    =     0.9482
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9207
Overall figure of merit              =     0.8469
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    127022.22       9100.9551       844258.56       844228.25    

 fvalues    127022.22       9100.9551       844251.50       844237.38    
 fvalues    127022.22       9100.9551       844251.50       844237.38    


     CGMAT cycle number =      8

 Weight matrix   0.38291252    
 Actual weight    6.5747271      is applied to the X-ray term


 function value    844245.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =    0.0003
Partial structure    1: scale =     0.3865, B  =   41.8257
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1879
Free R factor                        =     0.2302
Average Fourier shell correlation    =     0.9482
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9207
Overall figure of merit              =     0.8469
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    127023.95       9098.9629       844251.63       844237.38    

 fvalues    127023.95       9098.9629       844248.94       844246.75    
 fvalues    127023.95       9098.9629       844248.94       844246.75    


     CGMAT cycle number =      9

 Weight matrix   0.38285804    
 Actual weight    6.5747271      is applied to the X-ray term


 function value    844251.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =    0.0002
Partial structure    1: scale =     0.3865, B  =   41.8373
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1879
Free R factor                        =     0.2302
Average Fourier shell correlation    =     0.9482
AverageFree Fourier shell correlation=     0.9344
Average correlation coefficient      =     0.9207
Overall figure of merit              =     0.8469
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    127024.63       9099.1143       844250.81       844246.75    
 fvalues    127024.63       9099.1143       844250.81       844251.44    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   76
 Minimum acceptable grid spacing:    81   81  172
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   76
 Minimum acceptable grid spacing:    81   81  172
 Weight matrix   0.38282710    
 Actual weight    6.5747271      is applied to the X-ray term
Norm of X_ray positional gradient                43.8
Norm of Geom. positional gradient                43.8
Norm of X_ray B-factor gradient                  122.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.186E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.478E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8352E+06 GEOM=      9099.     TOTAL=     0.8443E+06
 function value    844250.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.860     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.802     5.000
Torsion angles, period  2. refined               90    35.046    22.778
Torsion angles, period  3. refined              268    13.191    15.000
Torsion angles, period  4. refined                9    12.497    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.247     0.200
VDW repulsions.others                          1351     0.196     0.200
VDW; torsion: refined_atoms                     726     0.174     0.200
VDW; torsion.others                             745     0.086     0.200
HBOND: refined_atoms                            215     0.204     0.200
HBOND.others                                      1     0.036     0.200
VDW repulsions: symmetry: refined_atoms           8     0.207     0.200
VDW repulsions: symmetry: others                 23     0.192     0.200
HBOND: symmetry: refined_atoms                   22     0.173     0.200
M. chain bond B values: refined atoms           746     1.749     1.471
M. chain bond B values: others                  746     1.744     1.472
M. chain angle B values: refined atoms          929     2.719     2.197
M. chain angle B values: others                 930     2.717     2.197
S. chain bond B values: refined atoms           811     3.123     1.871
S. chain bond B values: others                  810     3.118     1.871
S. chain angle B values: refined atoms         1177     4.757     2.639
S. chain angle B values: others                1178     4.755     2.639
Long range B values: refined atoms             1846     7.194    20.441
Long range B values: others                    1754     6.899    18.987
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =    0.0003
Partial structure    1: scale =     0.3865, B  =   41.8323
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.048    3427 100.00   439.5   448.8  0.16  0.17     158   440.0   449.4  0.20  0.21
 0.141    5763  99.98   269.3   255.3  0.17  0.15     333   274.6   254.1  0.22  0.20
 0.235    7390  99.99   179.1   162.0  0.18  0.16     400   183.0   166.4  0.21  0.18
 0.329    8616 100.00    79.8    93.8  0.30  0.23     463    74.9    89.5  0.35  0.28
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0475   2485   0.927    942   0.832   3427   0.901  0.952  0.9659  0.9728  0.9054  0.9376
  0.1415   4829   0.869    934   0.763   5763   0.852  1.010  0.9427  0.9561  0.8841  0.9386
  0.2355   6440   0.885    950   0.777   7390   0.871  1.057  0.9558  0.9619  0.9088  0.9411
  0.3294   7683   0.810    941   0.733   8624   0.802  0.788  0.8994  0.9213  0.8227  0.8846
 $$
Resolution limits                    =     41.964     1.630
Number of used reflections           =      25202
Percentage observed                  =    99.9887
Percentage of free reflections       =     5.0987
Overall R factor                     =     0.1879
Free R factor                        =     0.2302
Average Fourier shell correlation    =     0.9482
AverageFree Fourier shell correlation=     0.9344
Overall weighted R factor            =     0.1654
Free weighted R factor               =     0.2044
Overall weighted R2 factor           =     0.1968
Free weighted R2 factor              =     0.2405
Average correlation coefficient      =     0.9207
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9347
Cruickshanks DPI for coordinate error=     0.1000
DPI based on free R factor           =     0.1031
Overall figure of merit              =     0.8469
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8586
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    127024.42       9099.2695       844250.13       844251.44    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-63A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.860     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.802     5.000
Torsion angles, period  2. refined               90    35.046    22.778
Torsion angles, period  3. refined              268    13.193    15.000
Torsion angles, period  4. refined                9    12.497    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.247     0.200
VDW repulsions.others                          1352     0.195     0.200
VDW; torsion: refined_atoms                     726     0.174     0.200
VDW; torsion.others                             748     0.086     0.200
HBOND: refined_atoms                            215     0.204     0.200
HBOND.others                                      1     0.036     0.200
VDW repulsions: symmetry: refined_atoms           8     0.207     0.200
VDW repulsions: symmetry: others                 23     0.192     0.200
HBOND: symmetry: refined_atoms                   22     0.173     0.200
M. chain bond B values: refined atoms           746     1.749     1.471
M. chain bond B values: others                  746     1.744     1.471
M. chain angle B values: refined atoms          929     2.719     2.197
M. chain angle B values: others                 930     2.717     2.197
S. chain bond B values: refined atoms           811     3.123     1.871
S. chain bond B values: others                  810     3.118     1.871
S. chain angle B values: refined atoms         1177     4.757     2.639
S. chain angle B values: others                1178     4.755     2.639
Long range B values: refined atoms             1846     7.195    20.441
Long range B values: others                    1754     6.900    18.987
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0437, B  =    0.0002
Partial structure    1: scale =     0.3865, B  =   41.8242
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.048    3427 100.00   439.5   448.8  0.16  0.17     158   440.0   449.4  0.20  0.21
 0.141    5763  99.98   269.3   255.3  0.17  0.15     333   274.6   254.1  0.22  0.20
 0.235    7390  99.99   179.1   162.0  0.18  0.16     400   183.0   166.4  0.21  0.18
 0.329    8616 100.00    79.8    93.8  0.30  0.23     463    74.9    89.5  0.35  0.28
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0475   2485   0.927    942   0.832   3427   0.901  0.952  0.9659  0.9728  0.9054  0.9376
  0.1415   4829   0.869    934   0.763   5763   0.852  1.010  0.9426  0.9561  0.8841  0.9386
  0.2355   6440   0.885    950   0.777   7390   0.871  1.057  0.9557  0.9619  0.9088  0.9411
  0.3294   7683   0.810    941   0.733   8624   0.802  0.788  0.8994  0.9213  0.8228  0.8846
 $$
Resolution limits                    =     41.964     1.630
Number of used reflections           =      25202
Percentage observed                  =    99.9887
Percentage of free reflections       =     5.0987
Overall R factor                     =     0.1879
Free R factor                        =     0.2302
Average Fourier shell correlation    =     0.9482
AverageFree Fourier shell correlation=     0.9344
Overall weighted R factor            =     0.1654
Free weighted R factor               =     0.2044
Overall weighted R2 factor           =     0.1969
Free weighted R2 factor              =     0.2406
Average correlation coefficient      =     0.9207
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9346
Cruickshanks DPI for coordinate error=     0.1000
DPI based on free R factor           =     0.1031
Overall figure of merit              =     0.8469
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8586
-----------------------------------------------------------------------------
  Time in seconds: CPU =        22.77
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1881   0.2304   0.813      128118.    7047.4   0.0133  0.998   1.861  1.083   0.092
       1   0.1883   0.2299   0.844      127169.    7016.6   0.0122  0.914   1.793  1.042   0.087
       2   0.1878   0.2301   0.847      127050.    7014.3   0.0131  0.982   1.832  1.066   0.090
       3   0.1879   0.2302   0.847      127027.    7014.5   0.0133  0.991   1.848  1.076   0.091
       4   0.1879   0.2301   0.847      127022.    7014.7   0.0133  0.994   1.855  1.081   0.091
       5   0.1879   0.2301   0.847      127021.    7014.8   0.0133  0.994   1.857  1.082   0.091
       6   0.1879   0.2302   0.847      127022.    7015.0   0.0133  0.995   1.859  1.083   0.091
       7   0.1879   0.2302   0.847      127024.    7015.3   0.0133  0.995   1.859  1.083   0.091
       8   0.1879   0.2302   0.847      127025.    7015.3   0.0133  0.995   1.859  1.083   0.091
       9   0.1879   0.2302   0.847      127024.    7015.4   0.0133  0.995   1.860  1.083   0.091
      10   0.1879   0.2302   0.847      127025.    7015.4   0.0133  0.995   1.860  1.083   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1881   0.1879
             R free    0.2304   0.2302
     Rms BondLength    0.0133   0.0133
      Rms BondAngle    1.8615   1.8598
     Rms ChirVolume    0.0916   0.0912
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      54.9s System:    0.2s Elapsed:     0:56